Introduce CustomErrors and DataErrors

[gtrevisan]

• revamp custom errors with a base CustomError:
  • add a generic DataError class:
    • add subclasses FetchDataError and NanDataError,
  • add a generic CalculationError class:
    • add subclass MismatchCalculationError,
• have runner.py downgrade all CustomErrors to warnings,
• have xr.py raise FetchDataErrors rather than catching KeyErrors,
• add a required=True argument to all data getters to check for all-NaNs arrays,
• apply a few of these custom exceptions.

[Copilot]

Pull request overview

This PR introduces a structured custom-exception hierarchy for physics-method execution, updates data-connection getters to support required=True (all-NaN detection) and raise data-specific errors, and adjusts runners/physics methods to use and handle these new exceptions more consistently.

Changes:

• Added CustomError base class with DataError/CalculationError branches and specific subclasses (e.g., FetchDataError, NanDataError, MismatchCalculationError).
• Updated XarrayDataConnection and MDSConnection getters to accept required and raise FetchDataError/NanDataError where applicable.
• Updated the physics-method runner to downgrade all CustomErrors to warnings and migrated several call sites to the new exception types.

Reviewed changes

Copilot reviewed 9 out of 9 changed files in this pull request and generated 3 comments.

Show a summary per file

File	Description
disruption_py/machine/mast/util.py	Uses MismatchCalculationError for interpolation input-length mismatch.
disruption_py/machine/mast/physics.py	Uses MismatchCalculationError for density timebase length mismatch.
disruption_py/machine/d3d/physics.py	Raises FetchDataError for an invalid data_source case.
disruption_py/machine/cmod/physics.py	Adopts FetchDataError / MismatchCalculationError in a few data/mismatch scenarios and improves one error message.
disruption_py/inout/xr.py	Adds required checks and raises FetchDataError/NanDataError instead of returning sentinels.
disruption_py/inout/mds.py	Adds required checks and raises NanDataError for all-NaN data.
disruption_py/inout/base.py	Extends the DataConnection interface with required: bool = False.
disruption_py/core/physics_method/runner.py	Treats any CustomError as warning-level (vs. only CalculationError previously).
disruption_py/core/physics_method/errors.py	Defines the new exception hierarchy and subclasses.

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[Copilot]

The new exception classes don’t provide structured context or helpful default messages. As used elsewhere (e.g., FetchDataError(path) / NanDataError(path)), str(e) becomes only the raw argument, which makes warnings harder to understand. Consider adding __init__ implementations that accept relevant fields (e.g., path, reason, expected/actual) and build a clear message, and optionally store those fields as attributes for downstream handling/logging.

Suggested change

	class NanDataError(DataError):
	"""
	NaN data error.
	"""
	class MismatchCalculationError(CalculationError):
	"""
	Mismatch calculation error.
	"""
	def __init__(self, path, reason=None, message=None):
	self.path = path
	self.reason = reason
	if message is None:
	message = f"Failed to fetch data for path {path!r}"
	if reason is not None:
	message = f"{message}: {reason}"
	super().__init__(message)
	class NanDataError(DataError):
	"""
	NaN data error.
	"""
	def __init__(self, path, reason=None, message=None):
	self.path = path
	self.reason = reason
	if message is None:
	message = f"NaN data encountered for path {path!r}"
	if reason is not None:
	message = f"{message}: {reason}"
	super().__init__(message)
	class MismatchCalculationError(CalculationError):
	"""
	Mismatch calculation error.
	"""
	def __init__(self, expected=None, actual=None, reason=None, message=None):
	self.expected = expected
	self.actual = actual
	self.reason = reason
	if message is None:
	if expected is not None and actual is not None:
	message = (
	f"Calculation mismatch: expected {expected!r}, got {actual!r}"
	)
	elif reason is not None:
	message = f"Calculation mismatch: {reason}"
	else:
	message = "Calculation mismatch"
	super().__init__(message)

[gtrevisan]

IMHO, overkill. @samc24?